I have noticed that all of the orthologous genes (i am looking in remanei, brenneri, japonica i have tried so far) that when i click on download under the “transcript” portion of the page, that i am only getting the coding sequence, and not the full transcript sequence. Can someone help me with getting access to the transcript sequences?
Thanks,
Sarah
Hi Sarah, could you clarify what page you’re on? Are you looking at a particular gene page?
Cheers,
Chris
I am on the gene page for each gene i am working on. Under the sequence information, there is a tab to download next to “Transcript”. But when i click on it, it downloads CDS not the full transcript sequence. It has happened for ALL (at least 10 so far) of the genes, in brenneri, japonica, and remanei that i have looked.
OK, so you’re looking for the genomic sequence of the gene (exons + introns)?
I think the only way to get at this (right now) is from the genome browser like Paul Sternberg suggested in his e-mail. I would download the coding sequence as you have been, dump out the genomic sequence by selecting it from the genome browser, and performing a compare to make sure you have the ends right.
If you’re looking for UTRs, I don’t think we have that information available.
Thanks. You might want to add a note on the gene screen that has the download function for the transcript. It is not giving the full transcript, and unless you were looking at the length when you downloaded, you might not notice this. I would suggest disabling that download button until it is available. It is much easier to do it this way though, so if you can let me/folks know in the future if it is operational, that would be great.
Thanks for your help.
Hi Sarah, I’ve created a WormBase GitHub issue requesting the feature that you are describing. You can follow the issue here:
https://github.com/WormBase/website/issues/504
Hopefully we can get that up and running soon.
Cheers,
Chris